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MCL coexpression mm9:1294: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!5.54e-39!73;UBERON:0001016!2.32e-38!75;UBERON:0004121!3.19e-33!95;UBERON:0000924!3.19e-33!95;UBERON:0006601!3.19e-33!95;UBERON:0002346!5.02e-29!64;UBERON:0003075!5.02e-29!64;UBERON:0007284!5.02e-29!64;UBERON:0000073!3.80e-28!54;UBERON:0001049!1.37e-26!52;UBERON:0005068!1.37e-26!52;UBERON:0006241!1.37e-26!52;UBERON:0007135!1.37e-26!52;UBERON:0010371!4.42e-26!73;UBERON:0010314!2.30e-25!92;UBERON:0000955!5.67e-23!47;UBERON:0006238!5.67e-23!47;UBERON:0002616!1.27e-22!46;UBERON:0003056!8.14e-21!49;UBERON:0003080!4.33e-20!40;UBERON:0002020!6.90e-20!34;UBERON:0002780!1.04e-19!39;UBERON:0001890!1.04e-19!39;UBERON:0006240!1.04e-19!39;UBERON:0003528!1.95e-16!29;UBERON:0002791!1.95e-16!29;UBERON:0001893!1.95e-16!29;UBERON:0000956!8.99e-12!21;UBERON:0001869!8.99e-12!21;UBERON:0000203!8.99e-12!21;UBERON:0002619!1.01e-09!17;UBERON:0000025!1.67e-07!114;UBERON:0000468!3.66e-07!333;UBERON:0003076!5.21e-07!12;UBERON:0003057!5.21e-07!12;UBERON:0004111!5.64e-07!122
|ontology_enrichment_uberon=UBERON:0001017!5.54e-39!73;UBERON:0001016!2.32e-38!75;UBERON:0004121!3.19e-33!95;UBERON:0000924!3.19e-33!95;UBERON:0006601!3.19e-33!95;UBERON:0002346!5.02e-29!64;UBERON:0003075!5.02e-29!64;UBERON:0007284!5.02e-29!64;UBERON:0000073!3.80e-28!54;UBERON:0001049!1.37e-26!52;UBERON:0005068!1.37e-26!52;UBERON:0006241!1.37e-26!52;UBERON:0007135!1.37e-26!52;UBERON:0010371!4.42e-26!73;UBERON:0010314!2.30e-25!92;UBERON:0000955!5.67e-23!47;UBERON:0006238!5.67e-23!47;UBERON:0002616!1.27e-22!46;UBERON:0003056!8.14e-21!49;UBERON:0003080!4.33e-20!40;UBERON:0002020!6.90e-20!34;UBERON:0002780!1.04e-19!39;UBERON:0001890!1.04e-19!39;UBERON:0006240!1.04e-19!39;UBERON:0003528!1.95e-16!29;UBERON:0002791!1.95e-16!29;UBERON:0001893!1.95e-16!29;UBERON:0000956!8.99e-12!21;UBERON:0001869!8.99e-12!21;UBERON:0000203!8.99e-12!21;UBERON:0002619!1.01e-09!17;UBERON:0000025!1.67e-07!114;UBERON:0000468!3.66e-07!333;UBERON:0003076!5.21e-07!12;UBERON:0003057!5.21e-07!12;UBERON:0004111!5.64e-07!122
|tfbs_overrepresentation_for_novel_motifs=0.491922,0.819928,0.464605,0.535892,0.346849,0.550971,0.645383,0.247459,0.257202,0.283981,0.599767,0.632897,0.692139,0.6581,0.364314,0,0.856992,0.338549,0.656199,0.86893,0.426133,0.713088,0.657163,0.345236,0.472505,0.686615,0.63639,0.572827,0.394364,1.61954,0.558142,0.960397,0.336199,0.589948,0.364821,0.144368,0.871288,0.629145,0.303703,0.27383,0.342638,1.38433,0.327433,0.959963,0.368882,1.30113,0.77511,0.589246,0.0835644,0.397446,0.839084,1.69993,0.517905,1.10437,1.12205,0.66551,0.406788,0.619643,0.21472,2.69138,0.939962,0.724164,0.269393,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,1.1311,0.253541,4.64017,1.156,2.50016,0.57254,0.204132,0.763395,0.922432,0.430551,0.254777,2.03037,0.722675,0.240896,1.03903,2.7679,0.479018,0.181203,0.780154,1.77427,1.33021,2.37572,0.973447,0.35304,0.810643,0.281222,0.244935,2.23779,0.775372,0.160254,0.326561,0.960112,1.08669,0.839694,0.838613,2.36799,0.8998,0.585058,1.11115,0.428007,0.484547,1.0885,0.431734,0.605144,1.33732,0.340765,1.35637,0.53982,0.858327,0.322606,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,0.356163,1.06946,0.52828,1.2285,0.679647,1.35909,0.106956,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,1.83209,2.10357,1.25623,0.348692,0.183562,6.88983,1.10596,0.783181,0.678689,1.18867,0.71546,1.74506,0.48935,0.500417,1.31911,1.03816,0.926663,0.482185,0.82857,0.671017,1.56426,0.63125,0.131395
}}
}}

Revision as of 19:41, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr11:58752353..58752425,-p1@Rnf187
Mm9::chr16:18348274..18348366,+p2@Arvcf
Mm9::chr2:155102075..155102086,+p8@Map1lc3a
Mm9::chr5:34326128..34326178,+p1@Gm1673
Mm9::chr5:34326186..34326197,+p2@Gm1673
Mm9::chr7:25292246..25292259,+p6@Zfp428


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data


GO IDGO nameFDR corrected p-value
GO:0005776autophagic vacuole0.0394261229544641
GO:0016339calcium-dependent cell-cell adhesion0.0394261229544641



Relative expression of the co-expression cluster over median <br>Analyst:





Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
central nervous system5.54e-3973
nervous system2.32e-3875
ectoderm-derived structure3.19e-3395
ectoderm3.19e-3395
presumptive ectoderm3.19e-3395
neurectoderm5.02e-2964
neural plate5.02e-2964
presumptive neural plate5.02e-2964
regional part of nervous system3.80e-2854
neural tube1.37e-2652
neural rod1.37e-2652
future spinal cord1.37e-2652
neural keel1.37e-2652
ecto-epithelium4.42e-2673
structure with developmental contribution from neural crest2.30e-2592
brain5.67e-2347
future brain5.67e-2347
regional part of brain1.27e-2246
pre-chordal neural plate8.14e-2149
anterior neural tube4.33e-2040
gray matter6.90e-2034
regional part of forebrain1.04e-1939
forebrain1.04e-1939
future forebrain1.04e-1939
brain grey matter1.95e-1629
regional part of telencephalon1.95e-1629
telencephalon1.95e-1629
cerebral cortex8.99e-1221
cerebral hemisphere8.99e-1221
pallium8.99e-1221
regional part of cerebral cortex1.01e-0917
tube1.67e-07114
multi-cellular organism3.66e-07333
posterior neural tube5.21e-0712
chordal neural plate5.21e-0712
anatomical conduit5.64e-07122


TFBS overrepresentation<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data


Novel motifs




JASPAR motifs


Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}